The elastic properties of a molecule of duplex DNA are strongly dependent on nucleotide sequence. In the theory developed here the contribution c of the nth base-pair step to the elastic energy is assumed to be given by a function c̃ of six kinematical variables, called tilt, roll, twist, shift, slide, and rise, that describe the relative orientation and displacement of the nth and (n11)th base ...

Single stranded DNA (ssDNA) equilibrium dynamics are investigated using a fluorophore/quencher-labeled hairpin structure which thermally fluctuates between open and closed states. Temporal correlations of the fluorescence fluctuations are used to determine the energy barrier to conformational change. We find that ssDNA distortion is purely entropic for poly(T) but requires an additional enthalp...

In this study, we have examined the potential of second-generation antisense chimeric 2'-O-(2-methoxy)ethyl/DNA phosphorothioate oligonucleotides (ONs) to affect cell growth through non-antisense mechanisms. Evaluation of a series of ONs demonstrated that only a small number were cytotoxic at concentrations close to those required for antisense activity. Toxicity of the ONs appeared to be seque...

This paper studies a sequence-dependent scheduling problem incorporating order delivery, motivated by satellite imaging scheduling. A set of jobs is to be processed on a single machine and each job belongs to a specific group. The completion time of a group is the moment when all jobs belonging to this group are completed. The problem is to determine a processing sequence of the jobs such that ...

Recent single-molecule micromanipulation experiments on DNA subject to small distortion revealed positive coupling between DNA stretching and twisting--for instance, DNA elongates when overtwisted. Here we propose a method to calculate the twist-stretch coupling constant specific to a DNA fragment of a given sequence. The method employs a sequence-dependent dinucleotide force field and is based...

The flowshop scheduling problem with sequence dependent setup times is considered and shown to be NP-complete. A traveling salesman problem formulation is proposed for the case where jobs are processed continuously through the shop. These results are used to describe an approximate algorithm for the case where limited or infinite intermediate storage space is available to hold partially complet...

Harmonic elastic constants of 3-11 bp duplex DNA fragments were evaluated using four 5 ns unrestrained molecular dynamics simulation trajectories of 17 bp duplexes with explicit inclusion of solvent and counterions. All simulations were carried out with the Cornell et al. force-field and particle mesh Ewald method for long-range electrostatic interactions. The elastic constants including anisot...

A theoretical framework for prediction of the dynamic evolution of chemical species in DNA amplification reactions, for any specified sequence and operating conditions, is reported. Using the polymerase chain reaction (PCR) as an example, we developed a sequence- and temperature-dependent kinetic model for DNA amplification using first-principles biophysical modeling of DNA hybridization and po...

A Monte Carlo code applied to the cgDNA coarse-grain rigid-base model of B-form double-stranded DNA is used to predict a sequence-averaged persistence length of lF = 53.5 nm in the sense of Flory, and of lp = 160 bp or 53.5 nm in the sense of apparent tangent-tangent correlation decay. These estimates are slightly higher than the consensus experimental values of 150 bp or 50 nm, but we believe ...

bundles undergo deformations highly similar to a twisted rod under compression. Our data suggests that tau-like proteins minimize microtubule lattice interactions and the prevent torque generation that leads to extreme neuron deformations. These experimental results, together with mechanical modeling of the neuron, suggest that spectrin tension and microtubule bundle mechanics are crucial for s...